MIB-21306 Bioinformation Technology

Course

Credits 6.00

Assumed knowledge on:

Cell Biology I, Cell Biology 2 or Gentechnology

Continuation courses:

Genomics and Applied Bioinformatics

Contents:

The course is divided in 9 modules.
1. A general introduction to DNA- sequencing. In this chapter it is explained what we can and what we can not do with sequence analysis;
2. Introduction in Proteomics and Mass Spectrometry of peptides and proteins. An introduction of tandem mass spectrometry and an overview of its applications is given demonstrating the use of LC-MS data in finding/locating a gene/protein of interest;
3. Sequence alignments and database queries.
An introduction to text-mining tools, matrices and the FastA and Blast sequence comparison methods. Topics are sequence data pre-processing, the dynamic algorithms involved, E and init values and Bit, Z and Opt scores;
4. An introduction in transcriptomics. Topics are the construction of arrays, their usage and limitations. Real array data demonstrate how these data can be applied in solving biological questions;
5 Specialised Internet sites used for extracting topological signals;
6 Multiple sequence alignments. A tool used to clarify the function of an unknown protein, to aid in cloning a gene and to extract phylogenetic signals. Assumptions, limitations and pitfalls are discussed;
7 Annotation of sequences using web-based programs;
8 Protein structures. Comparison of three-dimensional protein structures and usage of structural databases, like CATH, SCOP, FSSP and MMDB;
9 Homology based three-dimensional modelling of proteins. Programs used are Insight II, What-check and Prosa.

Aims:

To give students an introduction into commonly used basic bioinformatics techniques and training in practical applications of these techniques in solving real research problems.

Activities:

Hands on course introductory lectures, training and study of relevant literature.

Examination:

Reading of papers (10%) a theoretical exam (45%) and an assignment (45%). The results of the 2-day assignment will be presented in the form of a report and an oral presentation.

Literature:

A syllabus and exercises are made available in electronic form (intraweb or CD-rom) during the course.